diff options
| -rw-r--r-- | wqflask/wqflask/show_trait/show_trait.py | 39 |
1 files changed, 25 insertions, 14 deletions
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py index a1e8f964..e958e78c 100644 --- a/wqflask/wqflask/show_trait/show_trait.py +++ b/wqflask/wqflask/show_trait/show_trait.py @@ -76,24 +76,35 @@ class ShowTrait: cellid=None) self.trait_vals = Redis.get(self.trait_id).split() - # ZS: Get verify/rna-seq link URLs + # Get verify/rna-seq link URLs try: - blatsequence = self.this_trait.blatseq + blatsequence = self.this_trait.blatseq if self.dataset.type == "ProbeSet" else self.this_trait.sequence if not blatsequence: # XZ, 06/03/2009: ProbeSet name is not unique among platforms. We should use ProbeSet Id instead. seqs = () - db_cursor.execute( - "SELECT Probe.Sequence, Probe.Name " - "FROM Probe, ProbeSet, ProbeSetFreeze, " - "ProbeSetXRef WHERE " - "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " - "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " - "ProbeSetFreeze.Name = %s AND " - "ProbeSet.Name = %s AND " - "Probe.ProbeSetId = ProbeSet.Id ORDER " - "BY Probe.SerialOrder", - (self.this_trait.dataset.name, self.this_trait.name,) - ) + if self.dataset.type == "ProbeSet": + db_cursor.execute( + "SELECT Probe.Sequence, Probe.Name " + "FROM Probe, ProbeSet, ProbeSetFreeze, " + "ProbeSetXRef WHERE " + "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " + "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " + "ProbeSetFreeze.Name = %s AND " + "ProbeSet.Name = %s AND " + "Probe.ProbeSetId = ProbeSet.Id ORDER " + "BY Probe.SerialOrder", + (self.this_trait.dataset.name, self.this_trait.name,) + ) + else: + db_cursor.execute( + "SELECT Geno.Sequence " + "FROM Geno, GenoXRef, GenoFreeze " + "WHERE Geno.Name = %s AND " + "Geno.Id = GenoXRef.GenoId AND " + "GenoXRef.GenoFreezeId = GenoFreeze.Id AND " + "GenoFreeze.Name = %s", + (self.this_trait.name, self.this_trait.dataset.name) + ) seqs = db_cursor.fetchall() if not seqs: raise ValueError |